Love this question, thanks R4DZER! My ecology-sensibilities are warning me that removing one bacteria from an ecosystem could have unpredictable knock-on effects…. but I’m going to go with C. diff (Clostridium difficile). It’s a really nasty bug that can cause infections in people in hospital, especially after a course of antibiotics, and is extremely difficult to get rid of once someone has it.
(Image credit: Wellcome Images)
(My cheat answer would be to get rid of antibiotic resistance genes – in many cases the bacteria itself isn’t the main problem, but the genes it has that make it resistant to antibiotics. They can share these with other bacteria and before you know it a relatively harmless E. coli can become a massive problem because it is infecting a loved one and is resistant to all our antibiotics)
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